Data Intake
| Index | stub | file | data_type | taxon_string | translation_table |
|---|---|---|---|---|---|
| 0 | KX808498-truncated | KX808498-truncated.gb | GenBank | Caulerpa_cliftonii_HV03798 | 11 |
| 1 | KY509313-truncated | KY509313-truncated.gb | GenBank | Avrainvillea_mazei_HV02664 | 11 |
| 2 | MH591083-truncated | MH591083-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 3 | MH591084-truncated | MH591084-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 4 | MH591085-truncated | MH591085-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 5 | NC_026795-truncated | NC_026795-truncated.txt | GenBank | Bryopsis_plumosa_WEST4718 | 11 |
| 6 | KY819064-truncated-cds | KY819064-truncated.cds.fasta | CDS | Chlorodesmis_fastigiata_HV03865 | 11 |
| 7 | KX808497-truncated | KX808497-truncated.fa | CDS | Derbesia_sp_WEST4838 | 11 |
Orthofinder
| Orthogroup | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| OG0000000 | Derbesia_sp_WEST4838|KX808497-truncated.fa|0|KX808497.1|petA | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|23|petA | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|0|petA | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|0|KY819064.1|petA | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|0|petA | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|0|petA |
| OG0000001 | Derbesia_sp_WEST4838|KX808497-truncated.fa|1|KX808497.1|rpl23 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|22|rpl23 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|3|rpl23 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|1|KY819064.1|rpl23 | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|1|rpl23 | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|1|rpl23 |
| OG0000002 | Derbesia_sp_WEST4838|KX808497-truncated.fa|2|KX808497.1|psaI | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|24|psaI | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|1|psaI | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|2|KY819064.1|psaI | Flabellia_petiolata_HV01202|MH591083-truncated.gb|1|psaI | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|2|psaI |
| OG0000003 | Derbesia_sp_WEST4838|KX808497-truncated.fa|3|KX808497.1|petG | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|26|petG | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|2|petG | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|3|KY819064.1|petG | Flabellia_petiolata_HV01202|MH591083-truncated.gb|0|petG | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|3|petG |
| OG0000004 | Derbesia_sp_WEST4838|KX808497-truncated.fa|4|KX808497.1|rbcL | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|27|rbcL | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|4|rbcL | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|4|KY819064.1|rbcL | Flabellia_petiolata_HV01202|MH591083-truncated.gb|2|rbcL | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|4|rbcL |
| OG0000005 | Derbesia_sp_WEST4838|KX808497-truncated.fa|6|KX808497.1|rps18 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|29|rps18, Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|30|orf179 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|5|rps18 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|6|KY819064.1|rps18 | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|6|rps18 |
| OG0000006 | Derbesia_sp_WEST4838|KX808497-truncated.fa|5|KX808497.1|psbE | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|28|psbE | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|6|psbE | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|5|KY819064.1|psbE | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|5|psbE |
| Orthogroup | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| OG0000007 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|0|rps9 | — | — | — | — | — | — |
| OG0000008 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|1|rpoC1 | — | — | — | — | — | — |
| OG0000009 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|2|rpoC2 | — | — | — | — | — | — |
| OG0000010 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|3|psaB | — | — | — | — | — | — |
| OG0000011 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|4|psbZ | — | — | — | — | — | — |
| OG0000012 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|5|orf180 | — | — | — | — | — | — |
| OG0000013 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|6|orf116 | — | — | — | — | — | — |
| OG0000014 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|7|orf144 | — | — | — | — | — | — |
| OG0000015 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|8|orf519 | — | — | — | — | — | — |
| OG0000016 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|9|psbA | — | — | — | — | — | — |
| OG0000017 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|10|orf128 | — | — | — | — | — | — |
| OG0000018 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|11|rpoA | — | — | — | — | — | — |
| OG0000019 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|12|rps11 | — | — | — | — | — | — |
| OG0000020 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|13|rpl36 | — | — | — | — | — | — |
| OG0000021 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|14|infA | — | — | — | — | — | — |
| OG0000022 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|15|rps8 | — | — | — | — | — | — |
| OG0000023 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|16|rpl5 | — | — | — | — | — | — |
| OG0000024 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|17|rpl14 | — | — | — | — | — | — |
| OG0000025 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|18|rpl16 | — | — | — | — | — | — |
| OG0000026 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|19|rps3 | — | — | — | — | — | — |
| OG0000027 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|20|rps19 | — | — | — | — | — | — |
| OG0000028 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|21|rpl2 | — | — | — | — | — | — |
| OG0000029 | — | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|25|ycf20 | — | — | — | — | — | — |
| OG0000030 | — | — | — | — | — | — | Flabellia_petiolata_HV01202|MH591085-truncated.gb|0|psbE | — |
| Input | KX808497-truncated.translated | KX808498-truncated.translated | KY509313-truncated.translated | KY819064-truncated-cds.translated | MH591083-truncated.translated | MH591084-truncated.translated | MH591085-truncated.translated | NC_026795-truncated.translated |
|---|---|---|---|---|---|---|---|---|
| KX808497-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KX808498-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KY509313-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| KY819064-truncated-cds.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
| MH591083-truncated.translated | 3 | 3 | 3 | 3 | 3 | 0 | 0 | 3 |
| MH591084-truncated.translated | 2 | 2 | 2 | 2 | 0 | 2 | 0 | 2 |
| MH591085-truncated.translated | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NC_026795-truncated.translated | 7 | 7 | 7 | 7 | 3 | 2 | 0 | 7 |
results/orthofinder/output/Orthogroup_Sequences/OG0000000.fa results/orthofinder/output/Orthogroup_Sequences/OG0000001.fa results/orthofinder/output/Orthogroup_Sequences/OG0000002.fa results/orthofinder/output/Orthogroup_Sequences/OG0000003.fa results/orthofinder/output/Orthogroup_Sequences/OG0000004.fa results/orthofinder/output/Orthogroup_Sequences/OG0000006.fa
results/orthofinder/orthosnap/OG0000005/OG0000005_orthosnap_0.fa
Alignment
results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa
Supermatrix
General Characteristics ======================= 6 Number of taxa 2388 Alignment length 496 Parsimony informative sites 496 Variable sites 1882 Constant sites Character Frequencies ===================== T 4524 G 2766 C 2251 A 4643 - 144
IQ-TREE 2.2.0.3 COVID-edition built Sep 5 2022
Input file name: results/supermatrix/supermatrix.cds.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 971247
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 6 sequences with 2388 nucleotide sites
Number of constant sites: 1400 (= 58.6265% of all sites)
Number of invariant (constant or ambiguous constant) sites: 1400 (= 58.6265% of all sites)
Number of parsimony informative sites: 496
Number of distinct site patterns: 492
ModelFinder
-----------
Best-fit model according to BIC: GTR+F+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
GTR+F+G4 -9950.622 19937.245 + 0.254 19937.534 + 0.257 20041.253 + 0.464
TIM2+F+G4 -9958.889 19949.778 - 0.000483 19950.007 - 0.000503 20042.229 + 0.285
TIM2+F+I -9960.089 19952.178 - 0.000145 19952.407 - 0.000152 20044.629 + 0.0857
GTR+F+I+G4 -9948.579 19935.159 + 0.721 19935.480 + 0.718 20044.945 + 0.0732
TIM2+F+I+G4 -9956.690 19947.381 - 0.0016 19947.639 - 0.00164 20045.610 + 0.0525
GTR+F+I -9953.065 19942.130 - 0.0221 19942.419 - 0.0224 20046.138 - 0.0403
TPM2u+F+I -9976.669 19983.337 - 2.49e-11 19983.540 - 2.63e-11 20070.011 - 2.64e-07
TVM+F+I -9969.542 19973.084 - 4.2e-09 19973.343 - 4.31e-09 20071.314 - 1.38e-07
TVM+F+G4 -9970.077 19974.155 - 2.46e-09 19974.413 - 2.52e-09 20072.384 - 8.05e-08
TPM2u+F+G4 -9978.794 19987.588 - 2.97e-12 19987.790 - 3.14e-12 20074.261 - 3.15e-08
TVM+F+I+G4 -9968.124 19972.249 - 6.37e-09 19972.537 - 6.45e-09 20076.256 - 1.16e-08
TIM+F+G4 -9976.342 19984.683 - 1.27e-11 19984.913 - 1.32e-11 20077.135 - 7.49e-09
TPM2u+F+I+G4 -9976.786 19985.571 - 8.15e-12 19985.801 - 8.49e-12 20078.023 - 4.81e-09
TIM+F+I -9978.268 19988.535 - 1.85e-12 19988.765 - 1.93e-12 20080.987 - 1.09e-09
TIM+F+I+G4 -9974.947 19983.894 - 1.89e-11 19984.152 - 1.94e-11 20082.123 - 6.18e-10
K3Pu+F+I -9994.574 20019.149 - 4.17e-19 20019.351 - 4.4e-19 20105.822 - 4.42e-15
K3Pu+F+G4 -9997.747 20025.495 - 1.75e-20 20025.697 - 1.84e-20 20112.168 - 1.85e-16
K3Pu+F+I+G4 -9996.293 20024.586 - 2.75e-20 20024.816 - 2.87e-20 20117.038 - 1.62e-17
TN+F+G4 -10003.782 20037.564 - 4.18e-23 20037.767 - 4.41e-23 20124.237 - 4.43e-19
TN+F+I -10005.761 20041.522 - 5.78e-24 20041.724 - 6.1e-24 20128.195 - 6.12e-20
TN+F+I+G4 -10002.313 20036.626 - 6.68e-23 20036.856 - 6.96e-23 20129.078 - 3.94e-20
TIM3+F+G4 -10003.134 20038.269 - 2.94e-23 20038.498 - 3.06e-23 20130.720 - 1.73e-20
TIM3+F+I -10004.794 20041.588 - 5.59e-24 20041.817 - 5.83e-24 20134.039 - 3.3e-21
TIM3+F+I+G4 -10001.831 20037.662 - 3.98e-23 20037.920 - 4.09e-23 20135.892 - 1.31e-21
HKY+F+I -10020.421 20068.842 - 6.75e-30 20069.019 - 7.22e-30 20149.737 - 1.29e-24
TPM3u+F+I -10019.385 20068.770 - 7e-30 20068.972 - 7.39e-30 20155.443 - 7.41e-26
HKY+F+G4 -10023.678 20075.356 - 2.6e-31 20075.533 - 2.78e-31 20156.251 - 4.95e-26
HKY+F+I+G4 -10022.196 20074.393 - 4.21e-31 20074.595 - 4.44e-31 20161.066 - 4.46e-27
TPM3u+F+G4 -10022.668 20075.336 - 2.63e-31 20075.538 - 2.77e-31 20162.009 - 2.78e-27
TPM3u+F+I+G4 -10021.313 20074.626 - 3.74e-31 20074.855 - 3.9e-31 20167.077 - 2.21e-28
F81+F+I -10041.407 20108.815 - 1.41e-38 20108.968 - 1.53e-38 20183.932 - 4.83e-32
F81+F+G4 -10046.374 20118.748 - 9.82e-41 20118.901 - 1.06e-40 20193.865 - 3.36e-34
F81+F+I+G4 -10044.860 20117.720 - 1.64e-40 20117.897 - 1.76e-40 20198.615 - 3.13e-35
SYM+I -10106.619 20243.238 - 9.11e-68 20243.440 - 9.62e-68 20329.911 - 9.66e-64
TVMe+I -10112.050 20252.100 - 1.08e-69 20252.277 - 1.16e-69 20332.995 - 2.07e-64
SYM+G4 -10109.264 20248.529 - 6.47e-69 20248.731 - 6.83e-69 20335.202 - 6.85e-65
SYM+I+G4 -10105.978 20243.957 - 6.36e-68 20244.186 - 6.63e-68 20336.408 - 3.75e-65
TVMe+G4 -10115.760 20259.521 - 2.65e-71 20259.698 - 2.84e-71 20340.416 - 5.06e-66
TVMe+I+G4 -10112.238 20254.477 - 3.31e-70 20254.679 - 3.49e-70 20341.150 - 3.5e-66
TIM2e+I -10159.736 20345.473 - 5.75e-90 20345.626 - 6.22e-90 20420.589 - 1.97e-83
TPM2+I -10164.413 20352.827 - 1.45e-91 20352.958 - 1.59e-91 20422.165 - 8.96e-84
TIM2e+I+G4 -10162.604 20353.209 - 1.2e-91 20353.386 - 1.29e-91 20434.104 - 2.29e-86
TIM2e+G4 -10166.496 20358.992 - 6.67e-93 20359.145 - 7.22e-93 20434.109 - 2.28e-86
TPM2+I+G4 -10167.174 20360.347 - 3.39e-93 20360.500 - 3.67e-93 20435.464 - 1.16e-86
TPM2+G4 -10171.099 20366.199 - 1.82e-94 20366.330 - 1.99e-94 20435.537 - 1.12e-86
TIMe+I -10187.704 20401.408 - 4.11e-102 20401.562 - 4.44e-102 20476.525 - 1.41e-95
K3P+I -10193.175 20410.349 - 4.7e-104 20410.480 - 5.14e-104 20479.688 - 2.89e-96
TIMe+G4 -10195.091 20416.182 - 2.54e-105 20416.335 - 2.75e-105 20491.298 - 8.71e-99
TIMe+I+G4 -10192.910 20413.821 - 8.28e-105 20413.998 - 8.86e-105 20494.716 - 1.58e-99
K3P+G4 -10203.234 20430.468 - 2.01e-108 20430.600 - 2.2e-108 20499.807 - 1.24e-100
K3P+I+G4 -10200.723 20427.446 - 9.11e-108 20427.600 - 9.86e-108 20502.563 - 3.12e-101
TIM3e+I -10233.779 20493.557 - 4.01e-122 20493.711 - 4.34e-122 20568.674 - 1.37e-115
TIM3e+G4 -10234.984 20495.968 - 1.2e-122 20496.121 - 1.3e-122 20571.085 - 4.12e-116
TPM3+I -10240.588 20505.176 - 1.2e-124 20505.307 - 1.32e-124 20574.515 - 7.41e-117
TIM3e+I+G4 -10233.164 20494.327 - 2.73e-122 20494.504 - 2.92e-122 20575.222 - 5.2e-117
TPM3+G4 -10246.096 20516.192 - 4.88e-127 20516.324 - 5.34e-127 20585.531 - 3e-119
TPM3+I+G4 -10243.636 20513.272 - 2.1e-126 20513.425 - 2.27e-126 20588.389 - 7.2e-120
GTR+F -10231.559 20497.118 - 6.77e-123 20497.376 - 6.95e-123 20595.348 - 2.22e-121
TNe+I -10266.205 20556.409 - 9.02e-136 20556.541 - 9.87e-136 20625.748 - 5.56e-128
JC+I -10275.298 20570.596 - 7.49e-139 20570.689 - 8.36e-139 20628.378 - 1.49e-128
K2P+I -10272.035 20566.071 - 7.2e-138 20566.182 - 7.96e-138 20629.631 - 7.97e-129
TNe+G4 -10273.280 20570.561 - 7.63e-139 20570.692 - 8.35e-139 20639.899 - 4.7e-131
TNe+I+G4 -10271.035 20568.070 - 2.65e-138 20568.223 - 2.87e-138 20643.186 - 9.08e-132
K2P+G4 -10281.744 20585.488 - 4.37e-142 20585.599 - 4.84e-142 20649.049 - 4.84e-133
JC+G4 -10285.852 20591.704 - 1.96e-143 20591.796 - 2.18e-143 20649.486 - 3.89e-133
K2P+I+G4 -10279.249 20582.498 - 1.95e-141 20582.630 - 2.14e-141 20651.837 - 1.2e-133
JC+I+G4 -10283.324 20588.649 - 9.01e-143 20588.760 - 9.96e-143 20652.209 - 9.97e-134
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: GTR+F+G4
Rate parameter R:
A-C: 2.6505
A-G: 2.9500
A-T: 3.9453
C-G: 1.9541
C-T: 6.1752
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.3273
pi(C) = 0.1587
pi(G) = 0.195
pi(T) = 0.319
Rate matrix Q:
A -0.9608 0.1793 0.2452 0.5363
C 0.3698 -1.372 0.1624 0.8394
G 0.4116 0.1322 -0.6797 0.1359
T 0.5504 0.4177 0.08311 -1.051
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.3949
Category Relative_rate Proportion
1 0.01598 0.25
2 0.1779 0.25
3 0.7257 0.25
4 3.08 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -9950.6201 (s.e. 142.9199)
Unconstrained log-likelihood (without tree): -9284.4483
Number of free parameters (#branches + #model parameters): 18
Akaike information criterion (AIC) score: 19937.2401
Corrected Akaike information criterion (AICc) score: 19937.5288
Bayesian information criterion (BIC) score: 20041.2479
Total tree length (sum of branch lengths): 1.0856
Sum of internal branch lengths: 0.2051 (18.8890% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Avrainvillea_mazei_HV02664' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+-----------------------------------------------Avrainvillea_mazei_HV02664
|
| +--------------------------------Bryopsis_plumosa_WEST4718
+----------------| (100)
| +-----------------------------------------Derbesia_sp_WEST4838
|
| +--------------------------------------Caulerpa_cliftonii_HV03798
+------------------| (100)
| +---------------------Chlorodesmis_fastigiata_HV03865
+---------| (98)
+----------------Flabellia_petiolata_HV01202
Tree in newick format:
(Avrainvillea_mazei_HV02664:0.2083414814,(Bryopsis_plumosa_WEST4718:0.1431662355,Derbesia_sp_WEST4838:0.1843593424)100:0.0749149837,(Caulerpa_cliftonii_HV03798:0.1700808743,(Chlorodesmis_fastigiata_HV03865:0.0968424549,Flabellia_petiolata_HV01202:0.0777150205)98:0.0437232892)100:0.0864126875);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -9950.620052
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+-----------------------------------------------Avrainvillea_mazei_HV02664
|
| +--------------------------------Bryopsis_plumosa_WEST4718
+----------------| (100)
| +-----------------------------------------Derbesia_sp_WEST4838
|
| +--------------------------------------Caulerpa_cliftonii_HV03798
+------------------| (100)
| +---------------------Chlorodesmis_fastigiata_HV03865
+---------| (98)
+----------------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Avrainvillea_mazei_HV02664:0.2083451843,(Bryopsis_plumosa_WEST4718:0.1431632239,Derbesia_sp_WEST4838:0.1843631022)100:0.0749217465,(Caulerpa_cliftonii_HV03798:0.1701007133,(Chlorodesmis_fastigiata_HV03865:0.0968536505,Flabellia_petiolata_HV01202:0.0777184196)98:0.0437063664)100:0.0864044150);
TIME STAMP
----------
Date and time: Thu Mar 7 15:44:23 2024
Total CPU time used: 1.19749 seconds (0h:0m:1s)
Total wall-clock time used: 1.290712833 seconds (0h:0m:1s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: 9350L-152779-M (AVX2, FMA3, 16 GB RAM)
Command: iqtree2 -s results/supermatrix/supermatrix.cds.fa -bb 1000 -m TEST -nt 1 -redo -pre results/supermatrix/supermatrix.cds
Seed: 971247 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 7 15:44:20 2024
Kernel: AVX+FMA - 1 threads (12 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/supermatrix/supermatrix.cds.fa ... Fasta format detected
Reading fasta file: done in 0.000672102 secs using 74.39% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00447011 secs using 48.21% CPU
Alignment has 6 sequences with 2388 columns, 492 distinct patterns
496 parsimony-informative, 492 singleton sites, 1399 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 3.19481e-05 secs using 81.38% CPU
1 Avrainvillea_mazei_HV02664 1.13% passed 34.31%
2 Bryopsis_plumosa_WEST4718 0.38% passed 73.08%
3 Caulerpa_cliftonii_HV03798 0.00% passed 67.19%
4 Chlorodesmis_fastigiata_HV03865 1.51% passed 91.03%
5 Derbesia_sp_WEST4838 0.63% passed 90.09%
6 Flabellia_petiolata_HV01202 2.39% passed 90.54%
**** TOTAL 1.01% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 4.19617e-05 secs using 73.88% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00199008 secs using 96.18% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -9948.592
Optimal log-likelihood: -9948.559
Rate parameters: A-C: 2.77621 A-G: 3.02265 A-T: 4.05715 C-G: 2.02910 C-T: 6.35200 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Proportion of invariable sites: 0.294
Gamma shape alpha: 0.898
Parameters optimization took 1 rounds (0.005 sec)
Time for fast ML tree search: 0.036 seconds
NOTE: ModelFinder requires 2 MB RAM!
ModelFinder will test up to 88 DNA models (sample size: 2388) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 10231.559 17 20497.118 20497.376 20595.348
2 GTR+F+I 9953.065 18 19942.130 19942.419 20046.138
3 GTR+F+G4 9950.622 18 19937.245 19937.534 20041.253
4 GTR+F+I+G4 9948.579 19 19935.159 19935.480 20044.945
6 SYM+I 10106.619 15 20243.238 20243.440 20329.911
7 SYM+G4 10109.264 15 20248.529 20248.731 20335.202
8 SYM+I+G4 10105.978 16 20243.957 20244.186 20336.408
10 TVM+F+I 9969.542 17 19973.084 19973.343 20071.314
11 TVM+F+G4 9970.077 17 19974.155 19974.413 20072.384
12 TVM+F+I+G4 9968.124 18 19972.249 19972.537 20076.256
14 TVMe+I 10112.050 14 20252.100 20252.277 20332.995
15 TVMe+G4 10115.760 14 20259.521 20259.698 20340.416
16 TVMe+I+G4 10112.238 15 20254.477 20254.679 20341.150
18 TIM3+F+I 10004.794 16 20041.588 20041.817 20134.039
19 TIM3+F+G4 10003.134 16 20038.269 20038.498 20130.720
20 TIM3+F+I+G4 10001.831 17 20037.662 20037.920 20135.892
22 TIM3e+I 10233.779 13 20493.557 20493.711 20568.674
23 TIM3e+G4 10234.984 13 20495.968 20496.121 20571.085
24 TIM3e+I+G4 10233.164 14 20494.327 20494.504 20575.222
26 TIM2+F+I 9960.089 16 19952.178 19952.407 20044.629
27 TIM2+F+G4 9958.889 16 19949.778 19950.007 20042.229
28 TIM2+F+I+G4 9956.690 17 19947.381 19947.639 20045.610
30 TIM2e+I 10159.736 13 20345.473 20345.626 20420.589
31 TIM2e+G4 10166.496 13 20358.992 20359.145 20434.109
32 TIM2e+I+G4 10162.604 14 20353.209 20353.386 20434.104
34 TIM+F+I 9978.268 16 19988.535 19988.765 20080.987
35 TIM+F+G4 9976.342 16 19984.683 19984.913 20077.135
36 TIM+F+I+G4 9974.947 17 19983.894 19984.152 20082.123
38 TIMe+I 10187.704 13 20401.408 20401.562 20476.525
39 TIMe+G4 10195.091 13 20416.182 20416.335 20491.298
40 TIMe+I+G4 10192.910 14 20413.821 20413.998 20494.716
42 TPM3u+F+I 10019.385 15 20068.770 20068.972 20155.443
43 TPM3u+F+G4 10022.668 15 20075.336 20075.538 20162.009
44 TPM3u+F+I+G4 10021.313 16 20074.626 20074.855 20167.077
46 TPM3+I 10240.588 12 20505.176 20505.307 20574.515
47 TPM3+G4 10246.096 12 20516.192 20516.324 20585.531
48 TPM3+I+G4 10243.636 13 20513.272 20513.425 20588.389
50 TPM2u+F+I 9976.669 15 19983.337 19983.540 20070.011
51 TPM2u+F+G4 9978.794 15 19987.588 19987.790 20074.261
52 TPM2u+F+I+G4 9976.786 16 19985.571 19985.801 20078.023
54 TPM2+I 10164.413 12 20352.827 20352.958 20422.165
55 TPM2+G4 10171.099 12 20366.199 20366.330 20435.537
56 TPM2+I+G4 10167.174 13 20360.347 20360.500 20435.464
58 K3Pu+F+I 9994.574 15 20019.149 20019.351 20105.822
59 K3Pu+F+G4 9997.747 15 20025.495 20025.697 20112.168
60 K3Pu+F+I+G4 9996.293 16 20024.586 20024.816 20117.038
62 K3P+I 10193.175 12 20410.349 20410.480 20479.688
63 K3P+G4 10203.234 12 20430.468 20430.600 20499.807
64 K3P+I+G4 10200.723 13 20427.446 20427.600 20502.563
66 TN+F+I 10005.761 15 20041.522 20041.724 20128.195
67 TN+F+G4 10003.782 15 20037.564 20037.767 20124.237
68 TN+F+I+G4 10002.313 16 20036.626 20036.856 20129.078
70 TNe+I 10266.205 12 20556.409 20556.541 20625.748
71 TNe+G4 10273.280 12 20570.561 20570.692 20639.899
72 TNe+I+G4 10271.035 13 20568.070 20568.223 20643.186
74 HKY+F+I 10020.421 14 20068.842 20069.019 20149.737
75 HKY+F+G4 10023.678 14 20075.356 20075.533 20156.251
76 HKY+F+I+G4 10022.196 15 20074.393 20074.595 20161.066
78 K2P+I 10272.035 11 20566.071 20566.182 20629.631
79 K2P+G4 10281.744 11 20585.488 20585.599 20649.049
80 K2P+I+G4 10279.249 12 20582.498 20582.630 20651.837
82 F81+F+I 10041.407 13 20108.815 20108.968 20183.932
83 F81+F+G4 10046.374 13 20118.748 20118.901 20193.865
84 F81+F+I+G4 10044.860 14 20117.720 20117.897 20198.615
86 JC+I 10275.298 10 20570.596 20570.689 20628.378
87 JC+G4 10285.852 10 20591.704 20591.796 20649.486
88 JC+I+G4 10283.324 11 20588.649 20588.760 20652.209
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: GTR+F+G4
Best-fit model: GTR+F+G4 chosen according to BIC
All model information printed to results/supermatrix/supermatrix.cds.model.gz
CPU time for ModelFinder: 0.810 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 1.011 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 971247)...
NOTE: 2 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -9950.622
Optimal log-likelihood: -9950.621
Rate parameters: A-C: 2.64999 A-G: 2.93589 A-T: 3.95010 C-G: 1.95186 C-T: 6.16638 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Gamma shape alpha: 0.395
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000181913 secs using 93.45% CPU
Computing ML distances took 0.000285 sec (of wall-clock time) 0.000245 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.38554e-05 secs using 79.75% CPU
Constructing RapidNJ tree: done in 3.40939e-05 secs using 105.6% CPU
Computing RapidNJ tree took 0.000155 sec (of wall-clock time) 0.000110 sec (of CPU time)
Log-likelihood of RapidNJ tree: -9985.567
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.069 second
Computing log-likelihood of 5 initial trees ... 0.005 seconds
Current best score: -9950.621
Do NNI search on 7 best initial trees
Optimizing NNI: done in 0.00325894 secs using 105.5% CPU
Optimizing NNI: done in 0.00630713 secs using 125.5% CPU
Optimizing NNI: done in 0.00906086 secs using 125.3% CPU
Optimizing NNI: done in 0.00493217 secs using 141.6% CPU
Optimizing NNI: done in 0.00747299 secs using 93.71% CPU
Optimizing NNI: done in 0.00720596 secs using 148.6% CPU
Optimizing NNI: done in 0.00912499 secs using 100.3% CPU
Finish initializing candidate tree set (7)
Current best tree score: -9950.621 / CPU time: 0.129
Number of iterations: 7
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00470519 secs using 175.6% CPU
Optimizing NNI: done in 0.00554609 secs using 160.5% CPU
Optimizing NNI: done in 0.00465822 secs using 161% CPU
Iteration 10 / LogL: -9950.648 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00412989 secs using 181.6% CPU
Optimizing NNI: done in 0.00743818 secs using 95.8% CPU
Optimizing NNI: done in 0.00906515 secs using 180.2% CPU
Optimizing NNI: done in 0.0055449 secs using 154% CPU
Optimizing NNI: done in 0.00588202 secs using 96.92% CPU
Optimizing NNI: done in 0.00401092 secs using 97.83% CPU
Optimizing NNI: done in 0.00686598 secs using 98.65% CPU
Optimizing NNI: done in 0.00650406 secs using 96.26% CPU
Optimizing NNI: done in 0.00964308 secs using 92.29% CPU
Optimizing NNI: done in 0.00567389 secs using 94.27% CPU
Iteration 20 / LogL: -9950.624 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00781894 secs using 88.16% CPU
UPDATE BEST LOG-LIKELIHOOD: -9950.621
Optimizing NNI: done in 0.011477 secs using 83.65% CPU
Optimizing NNI: done in 0.00939393 secs using 85.32% CPU
Optimizing NNI: done in 0.00393009 secs using 90.91% CPU
Optimizing NNI: done in 0.00698781 secs using 95.14% CPU
Optimizing NNI: done in 0.00323582 secs using 63.08% CPU
Optimizing NNI: done in 0.00807309 secs using 69.78% CPU
Optimizing NNI: done in 0.00458002 secs using 95.02% CPU
Optimizing NNI: done in 0.00369501 secs using 97.21% CPU
Optimizing NNI: done in 0.00707102 secs using 93.27% CPU
Iteration 30 / LogL: -9950.624 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00931716 secs using 90.89% CPU
Optimizing NNI: done in 0.00572896 secs using 83.51% CPU
Optimizing NNI: done in 0.00665689 secs using 87.52% CPU
Optimizing NNI: done in 0.00258017 secs using 99.68% CPU
Optimizing NNI: done in 0.00610518 secs using 98.75% CPU
UPDATE BEST LOG-LIKELIHOOD: -9950.621
Optimizing NNI: done in 0.00813794 secs using 93.89% CPU
Optimizing NNI: done in 0.00211692 secs using 93.86% CPU
Optimizing NNI: done in 0.00545907 secs using 98.77% CPU
Optimizing NNI: done in 0.00404811 secs using 97.95% CPU
Optimizing NNI: done in 0.00611401 secs using 99.12% CPU
Iteration 40 / LogL: -9950.684 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00346088 secs using 99.83% CPU
Optimizing NNI: done in 0.00384212 secs using 99.42% CPU
Optimizing NNI: done in 0.00173593 secs using 99.6% CPU
Optimizing NNI: done in 0.00697303 secs using 99.28% CPU
Optimizing NNI: done in 0.00451803 secs using 97.81% CPU
Optimizing NNI: done in 0.00281215 secs using 97.83% CPU
Optimizing NNI: done in 0.00701404 secs using 95.58% CPU
Optimizing NNI: done in 0.00167012 secs using 97% CPU
Optimizing NNI: done in 0.00530696 secs using 89.22% CPU
Optimizing NNI: done in 0.00440502 secs using 99.68% CPU
Iteration 50 / LogL: -9950.647 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -9979.321
Optimizing NNI: done in 0.00795817 secs using 91.89% CPU
Optimizing NNI: done in 0.00262904 secs using 89.46% CPU
Optimizing NNI: done in 0.00264287 secs using 98.11% CPU
Optimizing NNI: done in 0.00453711 secs using 97.82% CPU
Optimizing NNI: done in 0.00567698 secs using 97.34% CPU
Optimizing NNI: done in 0.00724888 secs using 92.22% CPU
Optimizing NNI: done in 0.00425005 secs using 96.05% CPU
Optimizing NNI: done in 0.006639 secs using 97.45% CPU
Optimizing NNI: done in 0.00816798 secs using 96.83% CPU
Optimizing NNI: done in 0.00628495 secs using 97.28% CPU
Iteration 60 / LogL: -9950.668 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00548697 secs using 98.42% CPU
Optimizing NNI: done in 0.00213099 secs using 99.86% CPU
Optimizing NNI: done in 0.00206995 secs using 95.9% CPU
Optimizing NNI: done in 0.00367284 secs using 98.59% CPU
Optimizing NNI: done in 0.00605106 secs using 97.37% CPU
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Optimizing NNI: done in 0.00638795 secs using 97.26% CPU
Optimizing NNI: done in 0.00437498 secs using 98.99% CPU
Optimizing NNI: done in 0.00450897 secs using 98.34% CPU
Optimizing NNI: done in 0.00137091 secs using 98.77% CPU
Iteration 70 / LogL: -9971.306 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00315309 secs using 99.71% CPU
Optimizing NNI: done in 0.00848103 secs using 97.16% CPU
Optimizing NNI: done in 0.00775003 secs using 97.29% CPU
Optimizing NNI: done in 0.00394487 secs using 97.32% CPU
Optimizing NNI: done in 0.00275183 secs using 97.03% CPU
Optimizing NNI: done in 0.00511503 secs using 98.81% CPU
Optimizing NNI: done in 0.00492811 secs using 96.3% CPU
Optimizing NNI: done in 0.00221109 secs using 97.33% CPU
Optimizing NNI: done in 0.00701404 secs using 97.63% CPU
Optimizing NNI: done in 0.00338602 secs using 99.82% CPU
Iteration 80 / LogL: -9950.624 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00449395 secs using 96.22% CPU
Optimizing NNI: done in 0.00811601 secs using 95.21% CPU
Optimizing NNI: done in 0.00457096 secs using 97.86% CPU
Optimizing NNI: done in 0.00685191 secs using 96.92% CPU
Optimizing NNI: done in 0.00493503 secs using 93.88% CPU
Optimizing NNI: done in 0.00694799 secs using 96.6% CPU
Optimizing NNI: done in 0.0107722 secs using 95.93% CPU
Optimizing NNI: done in 0.0061121 secs using 93.96% CPU
Optimizing NNI: done in 0.0060842 secs using 92.85% CPU
Optimizing NNI: done in 0.00735092 secs using 94.7% CPU
Iteration 90 / LogL: -9950.670 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0061419 secs using 96.48% CPU
Optimizing NNI: done in 0.00476313 secs using 97.92% CPU
Optimizing NNI: done in 0.00334191 secs using 96.53% CPU
Optimizing NNI: done in 0.00446987 secs using 98.91% CPU
Optimizing NNI: done in 0.00661278 secs using 88.18% CPU
Optimizing NNI: done in 0.00620794 secs using 88.34% CPU
Optimizing NNI: done in 0.00419712 secs using 99.59% CPU
Optimizing NNI: done in 0.00328493 secs using 97.05% CPU
Optimizing NNI: done in 0.00516295 secs using 98.47% CPU
Optimizing NNI: done in 0.00693417 secs using 98.51% CPU
Iteration 100 / LogL: -9950.712 / Time: 0h:0m:1s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -9979.321
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00236988 secs using 98.11% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -9950.621
Optimal log-likelihood: -9950.620
Rate parameters: A-C: 2.65045 A-G: 2.95002 A-T: 3.94530 C-G: 1.95408 C-T: 6.17521 G-T: 1.00000
Base frequencies: A: 0.327 C: 0.159 G: 0.195 T: 0.319
Gamma shape alpha: 0.395
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -9950.620
Creating bootstrap support values...
Split supports printed to NEXUS file results/supermatrix/supermatrix.cds.splits.nex
Total tree length: 1.086
Total number of iterations: 101
CPU time used for tree search: 1.109 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.181 sec (0h:0m:1s)
Total CPU time used: 1.197 sec (0h:0m:1s)
Total wall-clock time used: 1.278 sec (0h:0m:1s)
Computing bootstrap consensus tree...
Reading input file results/supermatrix/supermatrix.cds.splits.nex...
6 taxa and 12 splits.
Consensus tree written to results/supermatrix/supermatrix.cds.contree
Reading input trees file results/supermatrix/supermatrix.cds.contree
Log-likelihood of consensus tree: -9950.620
Analysis results written to:
IQ-TREE report: results/supermatrix/supermatrix.cds.iqtree
Maximum-likelihood tree: results/supermatrix/supermatrix.cds.treefile
Likelihood distances: results/supermatrix/supermatrix.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/supermatrix/supermatrix.cds.splits.nex
Consensus tree: results/supermatrix/supermatrix.cds.contree
Screen log file: results/supermatrix/supermatrix.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/supermatrix/supermatrix.cds.treefile -m "GTR{2.65045,2.95002,3.9453,1.95408,6.17521}+F{0.327341,0.1587,0.195008,0.318951}+G4{0.394866}" --length 2388
Date and Time: Thu Mar 7 15:44:23 2024
Gene Tree
OG0000004
IQ-TREE 2.2.0.3 COVID-edition built Sep 5 2022 Input file name: results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 739369 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 6 sequences with 1425 nucleotide sites Number of constant sites: 945 (= 66.3158% of all sites) Number of invariant (constant or ambiguous constant) sites: 945 (= 66.3158% of all sites) Number of parsimony informative sites: 247 Number of distinct site patterns: 273 ModelFinder ----------- Best-fit model according to BIC: GTR+F+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC GTR+F+G4 -5313.239 10662.478 + 0.637 10662.964 + 0.643 10757.193 + 0.902 GTR+F+I -5315.864 10667.729 - 0.0462 10668.215 - 0.0465 10762.444 + 0.0653 GTR+F+I+G4 -5312.939 10663.878 + 0.316 10664.419 + 0.311 10763.855 - 0.0323 SYM+G4 -5373.519 10777.038 - 8.47e-26 10777.379 - 9.19e-26 10855.967 - 3.21e-22 SYM+I -5373.847 10777.694 - 6.1e-26 10778.035 - 6.62e-26 10856.623 - 2.31e-22 SYM+I+G4 -5373.088 10778.176 - 4.8e-26 10778.562 - 5.09e-26 10862.367 - 1.31e-23 HKY+F+I -5389.886 10807.772 - 1.8e-32 10808.070 - 1.99e-32 10881.439 - 9.45e-28 HKY+F+G4 -5391.663 10811.326 - 3.04e-33 10811.624 - 3.37e-33 10884.993 - 1.6e-28 HKY+F+I+G4 -5392.647 10815.295 - 4.17e-34 10815.635 - 4.53e-34 10894.224 - 1.58e-30 F81+F+I -5407.874 10841.748 - 7.52e-40 10842.006 - 8.51e-40 10910.153 - 5.5e-34 F81+F+G4 -5410.576 10847.151 - 5.05e-41 10847.409 - 5.71e-41 10915.556 - 3.69e-35 F81+F+I+G4 -5411.633 10851.266 - 6.45e-42 10851.564 - 7.15e-42 10924.933 - 3.4e-37 GTR+F -5462.059 10958.118 - 4.05e-65 10958.553 - 4.19e-65 11047.570 - 7.96e-64 K2P+I -5487.031 10996.062 - 2.33e-73 10996.249 - 2.73e-73 11053.943 - 3.29e-65 JC+I -5493.624 11007.248 - 8.68e-76 11007.404 - 1.03e-75 11059.868 - 1.7e-66 K2P+G4 -5491.147 11004.293 - 3.8e-75 11004.480 - 4.46e-75 11062.175 - 5.36e-67 JC+G4 -5498.419 11016.839 - 7.18e-78 11016.994 - 8.54e-78 11069.458 - 1.41e-68 K2P+I+G4 -5492.024 11008.048 - 5.82e-76 11008.269 - 6.7e-76 11071.191 - 5.91e-69 JC+I+G4 -5499.410 11020.820 - 9.8e-79 11021.007 - 1.15e-78 11078.702 - 1.38e-70 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: GTR+F+G4 Rate parameter R: A-C: 1.9031 A-G: 2.4911 A-T: 4.8036 C-G: 1.1492 C-T: 7.7336 G-T: 1.0000 State frequencies: (empirical counts from alignment) pi(A) = 0.2978 pi(C) = 0.1621 pi(G) = 0.2254 pi(T) = 0.3147 Rate matrix Q: A -0.9788 0.1268 0.2307 0.6213 C 0.2329 -1.34 0.1064 1 G 0.3048 0.07655 -0.5107 0.1293 T 0.5878 0.5152 0.09262 -1.196 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.3265 Category Relative_rate Proportion 1 0.007692 0.25 2 0.1252 0.25 3 0.6378 0.25 4 3.229 0.25 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -5313.2364 (s.e. 110.0860) Unconstrained log-likelihood (without tree): -4731.2277 Number of free parameters (#branches + #model parameters): 18 Akaike information criterion (AIC) score: 10662.4728 Corrected Akaike information criterion (AICc) score: 10662.9593 Bayesian information criterion (BIC) score: 10757.1875 Total tree length (sum of branch lengths): 0.7900 Sum of internal branch lengths: 0.1578 (19.9696% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Derbesia_sp_WEST4838' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +------------| (95) | | | +---------------Chlorodesmis_fastigiata_HV03865 | | +----------| (98) | | +-----------------Flabellia_petiolata_HV01202 +--------------| (100) | +---------------------------------------Avrainvillea_mazei_HV02664 | +--------------------------Bryopsis_plumosa_WEST4718 Tree in newick format: (Derbesia_sp_WEST4838:0.1213215204,((Caulerpa_cliftonii_HV03798:0.1170328190,(Chlorodesmis_fastigiata_HV03865:0.0625957225,Flabellia_petiolata_HV01202:0.0719046281)98:0.0452561870)95:0.0513217711,Avrainvillea_mazei_HV02664:0.1543734236)100:0.0611901345,Bryopsis_plumosa_WEST4718:0.1050465395); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -5313.236393 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +------------| (95) | | | +---------------Chlorodesmis_fastigiata_HV03865 | | +----------| (98) | | +-----------------Flabellia_petiolata_HV01202 +--------------| (100) | +---------------------------------------Avrainvillea_mazei_HV02664 | +--------------------------Bryopsis_plumosa_WEST4718 Consensus tree in newick format: (Derbesia_sp_WEST4838:0.1213215378,((Caulerpa_cliftonii_HV03798:0.1170336985,(Chlorodesmis_fastigiata_HV03865:0.0625985454,Flabellia_petiolata_HV01202:0.0718943602)98:0.0452466890)95:0.0513171138,Avrainvillea_mazei_HV02664:0.1543670769)100:0.0611902465,Bryopsis_plumosa_WEST4718:0.1050435456); TIME STAMP ---------- Date and time: Thu Mar 7 15:44:19 2024 Total CPU time used: 0.968746 seconds (0h:0m:0s) Total wall-clock time used: 1.043941975 seconds (0h:0m:1s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: 9350L-152779-M (AVX2, FMA3, 16 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000004/OG0000004.cds -redo
Seed: 739369 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 7 15:44:17 2024
Kernel: AVX+FMA - 1 threads (12 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000004.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.000916958 secs using 45.37% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00287986 secs using 51.15% CPU
Alignment has 6 sequences with 1425 columns, 273 distinct patterns
247 parsimony-informative, 233 singleton sites, 944 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 3.50475e-05 secs using 77.04% CPU
1 Derbesia_sp_WEST4838 0.00% passed 97.69%
2 Caulerpa_cliftonii_HV03798 0.00% passed 49.86%
3 Avrainvillea_mazei_HV02664 0.00% passed 77.46%
4 Chlorodesmis_fastigiata_HV03865 0.00% passed 84.52%
5 Flabellia_petiolata_HV01202 0.00% passed 89.25%
6 Bryopsis_plumosa_WEST4718 0.00% passed 88.27%
**** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 4.48227e-05 secs using 69.16% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00119805 secs using 95.07% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -5312.975
Optimal log-likelihood: -5312.962
Rate parameters: A-C: 1.89811 A-G: 2.47143 A-T: 4.82573 C-G: 1.13587 C-T: 7.79940 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Proportion of invariable sites: 0.331
Gamma shape alpha: 0.791
Parameters optimization took 1 rounds (0.003 sec)
Time for fast ML tree search: 0.025 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 1425) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 5462.059 17 10958.118 10958.553 11047.570
2 GTR+F+I 5315.864 18 10667.729 10668.215 10762.444
3 GTR+F+G4 5313.239 18 10662.478 10662.964 10757.193
4 GTR+F+I+G4 5312.939 19 10663.878 10664.419 10763.855
6 SYM+I 5373.847 15 10777.694 10778.035 10856.623
7 SYM+G4 5373.519 15 10777.038 10777.379 10855.967
8 SYM+I+G4 5373.088 16 10778.176 10778.562 10862.367
10 HKY+F+I 5389.886 14 10807.772 10808.070 10881.439
11 HKY+F+G4 5391.663 14 10811.326 10811.624 10884.993
12 HKY+F+I+G4 5392.647 15 10815.295 10815.635 10894.224
14 K2P+I 5487.031 11 10996.062 10996.249 11053.943
15 K2P+G4 5491.147 11 11004.293 11004.480 11062.175
16 K2P+I+G4 5492.024 12 11008.048 11008.269 11071.191
18 F81+F+I 5407.874 13 10841.748 10842.006 10910.153
19 F81+F+G4 5410.576 13 10847.151 10847.409 10915.556
20 F81+F+I+G4 5411.633 14 10851.266 10851.564 10924.933
22 JC+I 5493.624 10 11007.248 11007.404 11059.868
23 JC+G4 5498.419 10 11016.839 11016.994 11069.458
24 JC+I+G4 5499.410 11 11020.820 11021.007 11078.702
Akaike Information Criterion: GTR+F+G4
Corrected Akaike Information Criterion: GTR+F+G4
Bayesian Information Criterion: GTR+F+G4
Best-fit model: GTR+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000004/OG0000004.cds.model.gz
CPU time for ModelFinder: 0.159 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.229 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 739369)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -5313.239
Optimal log-likelihood: -5313.237
Rate parameters: A-C: 1.90706 A-G: 2.48432 A-T: 4.80942 C-G: 1.14890 C-T: 7.71851 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Gamma shape alpha: 0.327
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000668049 secs using 59.43% CPU
Computing ML distances took 0.000813 sec (of wall-clock time) 0.000488 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.31402e-05 secs using 78.45% CPU
Constructing RapidNJ tree: done in 3.09944e-05 secs using 83.89% CPU
Computing RapidNJ tree took 0.000158 sec (of wall-clock time) 0.000098 sec (of CPU time)
Log-likelihood of RapidNJ tree: -5326.194
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.059 second
Computing log-likelihood of 5 initial trees ... 0.003 seconds
Current best score: -5313.237
Do NNI search on 7 best initial trees
Optimizing NNI: done in 0.00327301 secs using 79.07% CPU
Optimizing NNI: done in 0.00548291 secs using 91.63% CPU
Optimizing NNI: done in 0.00449705 secs using 122.6% CPU
Optimizing NNI: done in 0.00599313 secs using 101.4% CPU
Optimizing NNI: done in 0.00784302 secs using 80.93% CPU
Optimizing NNI: done in 0.00376797 secs using 184.6% CPU
Optimizing NNI: done in 0.00740695 secs using 85.33% CPU
Finish initializing candidate tree set (7)
Current best tree score: -5313.237 / CPU time: 0.108
Number of iterations: 7
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| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.00482011 secs using 168.8% CPU
Optimizing NNI: done in 0.00454783 secs using 185% CPU
Optimizing NNI: done in 0.00394416 secs using 120.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -5313.237
Iteration 10 / LogL: -5313.237 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0071919 secs using 109.8% CPU
Optimizing NNI: done in 0.0100012 secs using 74.7% CPU
Optimizing NNI: done in 0.00966191 secs using 84.18% CPU
Optimizing NNI: done in 0.0133541 secs using 64.76% CPU
Optimizing NNI: done in 0.0054369 secs using 96.73% CPU
Optimizing NNI: done in 0.00625801 secs using 83.01% CPU
Optimizing NNI: done in 0.00264406 secs using 94.97% CPU
Optimizing NNI: done in 0.00646996 secs using 62.24% CPU
Optimizing NNI: done in 0.00164223 secs using 87.87% CPU
Optimizing NNI: done in 0.006253 secs using 93.03% CPU
Iteration 20 / LogL: -5313.428 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00293994 secs using 96.33% CPU
Optimizing NNI: done in 0.00418591 secs using 90.23% CPU
Optimizing NNI: done in 0.00404191 secs using 94.19% CPU
Optimizing NNI: done in 0.00756192 secs using 97.04% CPU
Optimizing NNI: done in 0.00324798 secs using 99.26% CPU
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Optimizing NNI: done in 0.00227499 secs using 99.74% CPU
Optimizing NNI: done in 0.00110984 secs using 99.56% CPU
Optimizing NNI: done in 0.00436401 secs using 90.99% CPU
UPDATE BEST LOG-LIKELIHOOD: -5313.237
Optimizing NNI: done in 0.00216913 secs using 99.67% CPU
Iteration 30 / LogL: -5313.369 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00762105 secs using 96.22% CPU
Optimizing NNI: done in 0.00343299 secs using 97.09% CPU
Optimizing NNI: done in 0.00546408 secs using 94.71% CPU
Optimizing NNI: done in 0.00345993 secs using 93.35% CPU
Optimizing NNI: done in 0.00243092 secs using 96.55% CPU
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Optimizing NNI: done in 0.00350022 secs using 99.74% CPU
Optimizing NNI: done in 0.00221395 secs using 95.62% CPU
Iteration 40 / LogL: -5320.542 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00266099 secs using 99.14% CPU
Optimizing NNI: done in 0.00407887 secs using 95.59% CPU
Optimizing NNI: done in 0.00103593 secs using 99.62% CPU
Optimizing NNI: done in 0.00205517 secs using 99.65% CPU
Optimizing NNI: done in 0.00886893 secs using 91.66% CPU
Optimizing NNI: done in 0.00503898 secs using 98.59% CPU
Optimizing NNI: done in 0.00386214 secs using 99.69% CPU
Optimizing NNI: done in 0.00390506 secs using 98% CPU
Optimizing NNI: done in 0.00404811 secs using 98.19% CPU
Optimizing NNI: done in 0.00369406 secs using 98.46% CPU
Iteration 50 / LogL: -5313.348 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -5344.497
Optimizing NNI: done in 0.00446105 secs using 97.73% CPU
Optimizing NNI: done in 0.00404596 secs using 95.43% CPU
Optimizing NNI: done in 0.00341702 secs using 98.01% CPU
Optimizing NNI: done in 0.00615907 secs using 94.49% CPU
Optimizing NNI: done in 0.00746608 secs using 91.13% CPU
Optimizing NNI: done in 0.00423193 secs using 98.06% CPU
Optimizing NNI: done in 0.00312996 secs using 95.05% CPU
Optimizing NNI: done in 0.004498 secs using 92.13% CPU
Optimizing NNI: done in 0.00757718 secs using 87.92% CPU
Optimizing NNI: done in 0.00146794 secs using 99.8% CPU
Iteration 60 / LogL: -5320.542 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00550199 secs using 95.4% CPU
Optimizing NNI: done in 0.0027082 secs using 99.29% CPU
Optimizing NNI: done in 0.00391984 secs using 96.41% CPU
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Optimizing NNI: done in 0.00339198 secs using 98% CPU
Optimizing NNI: done in 0.00383377 secs using 98.86% CPU
Iteration 70 / LogL: -5313.320 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00667286 secs using 93.33% CPU
Optimizing NNI: done in 0.00459194 secs using 96.82% CPU
Optimizing NNI: done in 0.00433993 secs using 95.78% CPU
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Optimizing NNI: done in 0.00595689 secs using 97.65% CPU
Optimizing NNI: done in 0.00331998 secs using 97.29% CPU
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Optimizing NNI: done in 0.00514507 secs using 97.63% CPU
Iteration 80 / LogL: -5313.244 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00255489 secs using 97.19% CPU
Optimizing NNI: done in 0.00328016 secs using 99.45% CPU
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Optimizing NNI: done in 0.00516915 secs using 89.07% CPU
Iteration 90 / LogL: -5313.237 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00257897 secs using 99.5% CPU
Optimizing NNI: done in 0.00398588 secs using 90.34% CPU
Optimizing NNI: done in 0.00438309 secs using 97.21% CPU
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Optimizing NNI: done in 0.002244 secs using 98.71% CPU
Optimizing NNI: done in 0.00268197 secs using 90.64% CPU
Optimizing NNI: done in 0.00366211 secs using 93.22% CPU
Optimizing NNI: done in 0.00457692 secs using 97.03% CPU
Optimizing NNI: done in 0.0043509 secs using 96.78% CPU
Iteration 100 / LogL: -5313.244 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -5341.810
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00392699 secs using 94.19% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:1s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -5313.237
Optimal log-likelihood: -5313.236
Rate parameters: A-C: 1.90308 A-G: 2.49111 A-T: 4.80363 C-G: 1.14918 C-T: 7.73358 G-T: 1.00000
Base frequencies: A: 0.298 C: 0.162 G: 0.225 T: 0.315
Gamma shape alpha: 0.327
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -5313.236
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000004/OG0000004.cds.splits.nex
Total tree length: 0.790
Total number of iterations: 101
CPU time used for tree search: 0.901 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.938 sec (0h:0m:0s)
Total CPU time used: 0.969 sec (0h:0m:0s)
Total wall-clock time used: 1.034 sec (0h:0m:1s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000004/OG0000004.cds.splits.nex...
6 taxa and 15 splits.
Consensus tree written to results/gene_tree/OG0000004/OG0000004.cds.contree
Reading input trees file results/gene_tree/OG0000004/OG0000004.cds.contree
Log-likelihood of consensus tree: -5313.236
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000004/OG0000004.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000004/OG0000004.cds.treefile
Likelihood distances: results/gene_tree/OG0000004/OG0000004.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000004/OG0000004.cds.splits.nex
Consensus tree: results/gene_tree/OG0000004/OG0000004.cds.contree
Screen log file: results/gene_tree/OG0000004/OG0000004.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000004/OG0000004.cds.treefile -m "GTR{1.90308,2.49111,4.80363,1.14918,7.73358}+F{0.297778,0.162105,0.22538,0.314737}+G4{0.326523}" --length 1425
Date and Time: Thu Mar 7 15:44:19 2024
OG0000000
IQ-TREE 2.2.0.3 COVID-edition built Sep 5 2022 Input file name: results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 764725 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 6 sequences with 963 nucleotide sites Number of constant sites: 455 (= 47.2482% of all sites) Number of invariant (constant or ambiguous constant) sites: 455 (= 47.2482% of all sites) Number of parsimony informative sites: 249 Number of distinct site patterns: 334 ModelFinder ----------- Best-fit model according to BIC: HKY+F+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC HKY+F+G4 -4555.778 9139.556 - 0.00168 9139.999 - 0.00198 9207.737 + 0.769 HKY+F+I+G4 -4554.307 9138.614 - 0.00269 9139.121 - 0.00308 9211.665 + 0.108 HKY+F+I -4557.943 9143.885 - 0.000193 9144.328 - 0.000228 9212.066 + 0.0883 F81+F+G4 -4563.103 9152.205 - 3.01e-06 9152.589 - 3.66e-06 9215.516 - 0.0157 GTR+F+G4 -4546.645 9129.290 + 0.285 9130.015 + 0.292 9216.951 - 0.00768 F81+F+I -4564.150 9154.300 - 1.06e-06 9154.683 - 1.28e-06 9217.610 - 0.00552 F81+F+I+G4 -4561.524 9151.049 - 5.36e-06 9151.492 - 6.33e-06 9219.229 - 0.00246 GTR+F+I -4548.126 9132.253 + 0.0647 9132.977 + 0.0664 9219.914 - 0.00175 GTR+F+I+G4 -4544.825 9127.650 + 0.646 9128.456 + 0.636 9220.181 - 0.00153 GTR+F -4657.034 9348.067 - 8.86e-49 9348.715 - 9.44e-49 9430.858 - 2.73e-49 SYM+I -4671.878 9373.757 - 2.34e-54 9374.264 - 2.67e-54 9446.808 - 9.39e-53 SYM+G4 -4672.933 9375.865 - 8.15e-55 9376.372 - 9.32e-55 9448.916 - 3.27e-53 SYM+I+G4 -4670.387 9372.775 - 3.82e-54 9373.350 - 4.22e-54 9450.696 - 1.34e-53 JC+I -4729.397 9478.793 - 3.64e-77 9479.024 - 4.77e-77 9527.494 - 2.83e-70 JC+G4 -4732.692 9485.384 - 1.35e-78 9485.615 - 1.77e-78 9534.084 - 1.05e-71 K2P+I -4729.392 9480.784 - 1.34e-77 9481.062 - 1.72e-77 9534.355 - 9.16e-72 JC+I+G4 -4730.011 9482.022 - 7.24e-78 9482.300 - 9.28e-78 9535.593 - 4.93e-72 K2P+G4 -4732.683 9487.367 - 5e-79 9487.644 - 6.41e-79 9540.937 - 3.41e-73 K2P+I+G4 -4729.987 9483.975 - 2.73e-78 9484.303 - 3.41e-78 9542.415 - 1.63e-73 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: HKY+F+G4 Rate parameter R: A-C: 1.0000 A-G: 1.5194 A-T: 1.0000 C-G: 1.0000 C-T: 1.5194 G-T: 1.0000 State frequencies: (empirical counts from alignment) pi(A) = 0.3722 pi(C) = 0.1535 pi(G) = 0.1489 pi(T) = 0.3253 Rate matrix Q: A -0.8606 0.1874 0.2762 0.3971 C 0.4543 -1.239 0.1818 0.6033 G 0.6902 0.1874 -1.275 0.3971 T 0.4543 0.2847 0.1818 -0.9207 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.551 Category Relative_rate Proportion 1 0.04318 0.25 2 0.2839 0.25 3 0.8541 0.25 4 2.819 0.25 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -4555.7776 (s.e. 87.9063) Unconstrained log-likelihood (without tree): -4137.8401 Number of free parameters (#branches + #model parameters): 14 Akaike information criterion (AIC) score: 9139.5551 Corrected Akaike information criterion (AICc) score: 9139.9982 Bayesian information criterion (BIC) score: 9207.7359 Total tree length (sum of branch lengths): 1.5812 Sum of internal branch lengths: 0.2811 (17.7808% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Derbesia_sp_WEST4838' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +-------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +-----------------| (100) | | | +----------------Chlorodesmis_fastigiata_HV03865 | | +--| (61) | | +--------Flabellia_petiolata_HV01202 +----------| (81) | +---------------------------------Avrainvillea_mazei_HV02664 | +---------------------Bryopsis_plumosa_WEST4718 Tree in newick format: (Derbesia_sp_WEST4838:0.2868134729,((Caulerpa_cliftonii_HV03798:0.2728583496,(Chlorodesmis_fastigiata_HV03865:0.1539893514,Flabellia_petiolata_HV01202:0.0808824659)61:0.0223456147)100:0.1607566746,Avrainvillea_mazei_HV02664:0.3080387618)81:0.0980409243,Bryopsis_plumosa_WEST4718:0.1974356402); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -4555.777559 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +-------------------------------Derbesia_sp_WEST4838 | | +-----------------------------Caulerpa_cliftonii_HV03798 | +-----------------| (100) | | | +----------------Chlorodesmis_fastigiata_HV03865 | | +--| (61) | | +--------Flabellia_petiolata_HV01202 +----------| (81) | +---------------------------------Avrainvillea_mazei_HV02664 | +---------------------Bryopsis_plumosa_WEST4718 Consensus tree in newick format: (Derbesia_sp_WEST4838:0.2868207215,((Caulerpa_cliftonii_HV03798:0.2729563013,(Chlorodesmis_fastigiata_HV03865:0.1540181581,Flabellia_petiolata_HV01202:0.0809055226)61:0.0222753283)100:0.1607877511,Avrainvillea_mazei_HV02664:0.3080731129)81:0.0980499302,Bryopsis_plumosa_WEST4718:0.1974507790); TIME STAMP ---------- Date and time: Thu Mar 7 15:44:19 2024 Total CPU time used: 1.120203 seconds (0h:0m:1s) Total wall-clock time used: 1.229127884 seconds (0h:0m:1s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: 9350L-152779-M (AVX2, FMA3, 16 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000000/OG0000000.cds -redo
Seed: 764725 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 7 15:44:17 2024
Kernel: AVX+FMA - 1 threads (12 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_cds/OG0000000.trimmed.cds.alignment.fa ... Fasta format detected
Reading fasta file: done in 0.00027895 secs using 83.89% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00179911 secs using 55.64% CPU
Alignment has 6 sequences with 963 columns, 334 distinct patterns
249 parsimony-informative, 259 singleton sites, 455 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 3.29018e-05 secs using 79.02% CPU
1 Derbesia_sp_WEST4838 1.56% passed 91.88%
2 Caulerpa_cliftonii_HV03798 0.00% passed 98.01%
3 Avrainvillea_mazei_HV02664 2.80% passed 18.77%
4 Chlorodesmis_fastigiata_HV03865 3.74% passed 85.62%
5 Flabellia_petiolata_HV01202 5.92% passed 93.93%
6 Bryopsis_plumosa_WEST4718 0.93% passed 76.72%
**** TOTAL 2.49% 0 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 3.88622e-05 secs using 69.48% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00161409 secs using 89.77% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -4544.868
Optimal log-likelihood: -4544.854
Rate parameters: A-C: 2.70521 A-G: 3.27681 A-T: 2.57568 C-G: 3.15656 C-T: 3.89217 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Proportion of invariable sites: 0.241
Gamma shape alpha: 1.205
Parameters optimization took 1 rounds (0.003 sec)
Time for fast ML tree search: 0.018 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 24 DNA models (sample size: 963) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 4657.034 17 9348.067 9348.715 9430.858
2 GTR+F+I 4548.126 18 9132.253 9132.977 9219.914
3 GTR+F+G4 4546.645 18 9129.290 9130.015 9216.951
4 GTR+F+I+G4 4544.825 19 9127.650 9128.456 9220.181
6 SYM+I 4671.878 15 9373.757 9374.264 9446.808
7 SYM+G4 4672.933 15 9375.865 9376.372 9448.916
8 SYM+I+G4 4670.387 16 9372.775 9373.350 9450.696
10 HKY+F+I 4557.943 14 9143.885 9144.328 9212.066
11 HKY+F+G4 4555.778 14 9139.556 9139.999 9207.737
12 HKY+F+I+G4 4554.307 15 9138.614 9139.121 9211.665
14 K2P+I 4729.392 11 9480.784 9481.062 9534.355
15 K2P+G4 4732.683 11 9487.367 9487.644 9540.937
16 K2P+I+G4 4729.987 12 9483.975 9484.303 9542.415
18 F81+F+I 4564.150 13 9154.300 9154.683 9217.610
19 F81+F+G4 4563.103 13 9152.205 9152.589 9215.516
20 F81+F+I+G4 4561.524 14 9151.049 9151.492 9219.229
22 JC+I 4729.397 10 9478.793 9479.024 9527.494
23 JC+G4 4732.692 10 9485.384 9485.615 9534.084
24 JC+I+G4 4730.011 11 9482.022 9482.300 9535.593
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: HKY+F+G4
Best-fit model: HKY+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000000/OG0000000.cds.model.gz
CPU time for ModelFinder: 0.186 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.244 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 764725)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -4555.778
Optimal log-likelihood: -4555.778
Rate parameters: A-C: 1.00000 A-G: 1.51915 A-T: 1.00000 C-G: 1.00000 C-T: 1.51915 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Gamma shape alpha: 0.552
Parameters optimization took 1 rounds (0.005 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000280857 secs using 92.93% CPU
Computing ML distances took 0.000420 sec (of wall-clock time) 0.000359 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.60012e-05 secs using 77.78% CPU
Constructing RapidNJ tree: done in 3.09944e-05 secs using 109.7% CPU
Computing RapidNJ tree took 0.000148 sec (of wall-clock time) 0.000118 sec (of CPU time)
Log-likelihood of RapidNJ tree: -4555.778
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| INITIALIZING CANDIDATE TREE SET |
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Generating 99 parsimony trees... 0.061 second
Computing log-likelihood of 6 initial trees ... 0.004 seconds
Current best score: -4555.778
Do NNI search on 7 best initial trees
Optimizing NNI: done in 0.00181484 secs using 189.5% CPU
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Optimizing NNI: done in 0.00699806 secs using 93.97% CPU
Finish initializing candidate tree set (7)
Current best tree score: -4555.778 / CPU time: 0.115
Number of iterations: 7
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| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.00453997 secs using 172.5% CPU
Optimizing NNI: done in 0.00663781 secs using 92.03% CPU
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Iteration 10 / LogL: -4555.821 / Time: 0h:0m:0s
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Iteration 20 / LogL: -4555.779 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00631595 secs using 94.63% CPU
Optimizing NNI: done in 0.00281405 secs using 99.22% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.00391793 secs using 96.84% CPU
Optimizing NNI: done in 0.00336218 secs using 94.94% CPU
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Optimizing NNI: done in 0.00290608 secs using 97.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.00382113 secs using 96.1% CPU
Optimizing NNI: done in 0.00607419 secs using 98.63% CPU
Iteration 30 / LogL: -4555.780 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00647497 secs using 94.41% CPU
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Iteration 40 / LogL: -4555.789 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00444913 secs using 98.92% CPU
Optimizing NNI: done in 0.00616288 secs using 94.5% CPU
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Optimizing NNI: done in 0.00457907 secs using 98.8% CPU
Iteration 50 / LogL: -4555.781 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4579.294
Optimizing NNI: done in 0.00447202 secs using 90.21% CPU
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Optimizing NNI: done in 0.00634289 secs using 93.11% CPU
Iteration 60 / LogL: -4555.780 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00509501 secs using 98.39% CPU
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Iteration 70 / LogL: -4555.788 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00420594 secs using 98.27% CPU
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Iteration 80 / LogL: -4555.822 / Time: 0h:0m:0s (0h:0m:0s left)
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Optimizing NNI: done in 0.00347495 secs using 97.38% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
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Iteration 90 / LogL: -4555.792 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00495601 secs using 96.75% CPU
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Optimizing NNI: done in 0.0050869 secs using 94.58% CPU
UPDATE BEST LOG-LIKELIHOOD: -4555.778
Optimizing NNI: done in 0.00758719 secs using 92.67% CPU
Optimizing NNI: done in 0.0042429 secs using 96.56% CPU
Optimizing NNI: done in 0.00915504 secs using 90.77% CPU
Optimizing NNI: done in 0.00638294 secs using 88.88% CPU
Optimizing NNI: done in 0.00758195 secs using 92.46% CPU
Optimizing NNI: done in 0.00538492 secs using 91.83% CPU
Iteration 100 / LogL: -4555.791 / Time: 0h:0m:1s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4579.294
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.011929 secs using 73.75% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:1s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4555.778
Optimal log-likelihood: -4555.778
Rate parameters: A-C: 1.00000 A-G: 1.51939 A-T: 1.00000 C-G: 1.00000 C-T: 1.51939 G-T: 1.00000
Base frequencies: A: 0.372 C: 0.154 G: 0.149 T: 0.325
Gamma shape alpha: 0.551
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -4555.778
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000000/OG0000000.cds.splits.nex
Total tree length: 1.581
Total number of iterations: 101
CPU time used for tree search: 1.048 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.101 sec (0h:0m:1s)
Total CPU time used: 1.120 sec (0h:0m:1s)
Total wall-clock time used: 1.217 sec (0h:0m:1s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000000/OG0000000.cds.splits.nex...
6 taxa and 13 splits.
Consensus tree written to results/gene_tree/OG0000000/OG0000000.cds.contree
Reading input trees file results/gene_tree/OG0000000/OG0000000.cds.contree
Log-likelihood of consensus tree: -4555.778
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000000/OG0000000.cds.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000000/OG0000000.cds.treefile
Likelihood distances: results/gene_tree/OG0000000/OG0000000.cds.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000000/OG0000000.cds.splits.nex
Consensus tree: results/gene_tree/OG0000000/OG0000000.cds.contree
Screen log file: results/gene_tree/OG0000000/OG0000000.cds.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000000/OG0000000.cds.treefile -m "HKY{1.51939}+F{0.372204,0.153532,0.148917,0.325346}+G4{0.550981}" --length 963
Date and Time: Thu Mar 7 15:44:19 2024
Supertree
Workflow
Bibliography
- 1
- Deren A. R. Eaton. Toytree: A minimalist tree visualization and manipulation library for Python. Methods in Ecology and Evolution, 11:187–191, 2020. doi:10.1111/2041-210X.13313.
- 2
- David M. Emms and Steven Kelly. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1):238, 2019. URL: https://doi.org/10.1186/s13059-019-1832-y, doi:10.1186/s13059-019-1832-y.
- 3
- Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2):518–522, 10 2017. URL: https://doi.org/10.1093/molbev/msx281, arXiv:https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf, doi:10.1093/molbev/msx281.
- 4
- Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, and Lars S Jermiin. Modelfinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6):587–589, 2017. URL: https://doi.org/10.1038/nmeth.4285, doi:10.1038/nmeth.4285.
- 5
- Kazutaka Katoh and Daron M. Standley. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4):772–780, 01 2013. URL: https://doi.org/10.1093/molbev/mst010, arXiv:https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf, doi:10.1093/molbev/mst010.
- 6
- Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, and Robert Lanfear. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5):1530–1534, 02 2020. URL: https://doi.org/10.1093/molbev/msaa015, arXiv:https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf, doi:10.1093/molbev/msaa015.
- 7
- Jacob L Steenwyk, III Buida, Thomas J, Abigail L Labella, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics, 37(16):2325–2331, 02 2021. URL: https://doi.org/10.1093/bioinformatics/btab096, arXiv:https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf, doi:10.1093/bioinformatics/btab096.
- 8
- Jacob L. Steenwyk, Thomas J. Buida, Carla Gonçalves, Dayna C. Goltz, Grace Morales, Matthew E. Mead, Abigail L. LaBella, Christina M. Chavez, Jonathan E. Schmitz, Maria Hadjifrangiskou, Yuanning Li, and Antonis Rokas. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. biorxiv, oct 2021. URL: https://doi.org/10.1101%2F2021.10.02.462868, doi:10.1101/2021.10.02.462868.
- 9
- Jacob L. Steenwyk, Thomas J. Buida, III, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. Clipkit: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology, 18(12):1–17, 12 2020. URL: https://doi.org/10.1371/journal.pbio.3001007, doi:10.1371/journal.pbio.3001007.
- 10
- Chao Zhang, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. Astral-iii: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6):153, 2018. URL: https://doi.org/10.1186/s12859-018-2129-y, doi:10.1186/s12859-018-2129-y.
@article{10.1093/molbev/mst010,
author = "Katoh, Kazutaka and Standley, Daron M.",
title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
journal = "Molecular Biology and Evolution",
volume = "30",
number = "4",
pages = "772-780",
year = "2013",
month = "01",
abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
issn = "0737-4038",
doi = "10.1093/molbev/mst010",
url = "https://doi.org/10.1093/molbev/mst010",
eprint = "https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf"
}
@article{Emms2019,
author = "Emms, David M. and Kelly, Steven",
type = "Journal Article",
title = "OrthoFinder: phylogenetic orthology inference for comparative genomics",
journal = "Genome Biology",
number = "1",
doi = "10.1186/s13059-019-1832-y",
volume = "20",
pages = "238",
url = "https://doi.org/10.1186/s13059-019-1832-y",
year = "2019",
abstract = "Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.",
isbn = "1474-760X",
DA = "2019/11/14"
}
@article{10.1371/journal.pbio.3001007,
author = "Steenwyk, Jacob L. and Buida, III, Thomas J. and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
doi = "10.1371/journal.pbio.3001007",
journal = "PLOS Biology",
publisher = "Public Library of Science",
title = "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference",
year = "2020",
month = "12",
volume = "18",
url = "https://doi.org/10.1371/journal.pbio.3001007",
pages = "1-17",
abstract = "Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.",
number = "12"
}
@article{Steenwyk_2021,
author = "Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis",
doi = "10.1101/2021.10.02.462868",
url = "https://doi.org/10.1101\%2F2021.10.02.462868",
year = "2021",
month = "oct",
journal = "biorxiv",
publisher = "Cold Spring Harbor Laboratory",
title = "{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data"
}
@article{10.1093/molbev/msx281,
author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
journal = "Molecular Biology and Evolution",
volume = "35",
number = "2",
pages = "518-522",
year = "2017",
month = "10",
abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
issn = "0737-4038",
doi = "10.1093/molbev/msx281",
url = "https://doi.org/10.1093/molbev/msx281",
eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}
@article{10.1093/bioinformatics/btab096,
author = "Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
journal = "Bioinformatics",
volume = "37",
number = "16",
pages = "2325-2331",
year = "2021",
month = "02",
abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
issn = "1367-4803",
doi = "10.1093/bioinformatics/btab096",
url = "https://doi.org/10.1093/bioinformatics/btab096",
eprint = "https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf"
}
@article{eaton_toytree_2020,
author = "Eaton, Deren A. R.",
title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
volume = "11",
doi = "10.1111/2041-210X.13313",
journal = "Methods in Ecology and Evolution",
year = "2020",
pages = "187--191"
}
@article{10.1093/molbev/msaa015,
author = "Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert",
title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
journal = "Molecular Biology and Evolution",
volume = "37",
number = "5",
pages = "1530-1534",
year = "2020",
month = "02",
abstract = "{IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.}",
issn = "0737-4038",
doi = "10.1093/molbev/msaa015",
url = "https://doi.org/10.1093/molbev/msaa015",
eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}
@article{Kalyaanamoorthy2017,
author = "Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas K F and von Haeseler, Arndt and Jermiin, Lars S",
type = "Journal Article",
title = "ModelFinder: fast model selection for accurate phylogenetic estimates",
journal = "Nature Methods",
number = "6",
doi = "10.1038/nmeth.4285",
volume = "14",
pages = "587--589",
url = "https://doi.org/10.1038/nmeth.4285",
year = "2017",
abstract = "ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.",
issn = "1548-7105",
DA = "2017/06/01"
}
@article{Zhang2018,
author = "Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash",
type = "Journal Article",
title = "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees",
journal = "BMC Bioinformatics",
number = "6",
doi = "10.1186/s12859-018-2129-y",
volume = "19",
pages = "153",
url = "https://doi.org/10.1186/s12859-018-2129-y",
year = "2018",
abstract = "Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.",
issn = "1471-2105",
DA = "2018/05/08"
}File(s) not Fasta or Genbank file. Suffix from file 'NC_026795-truncated.txt' is not Fasta or Genbank. File is assumed to be in Fasta format.